i bought this bike a week and a half ago and i've been trying to put the lights and wiring back together after the previous owner took them off. i believe i have connected the battery+ to the red wire that runs to the rectifier, but there is another red wire in that area by the oil tank, and it has a male and female end. 
can someone tell me what they do / where they go?

Three reds.  Two go to factory fuse holder.  Third to battery.  Probably a few dozen threads with pictures on this topic if you search. 

Someone will correct me if I'm wrong but pretty sure two harness females connect to fuse holder and male harness to battery. 

Yes 2 females to fuse holder that’s what I did 

How I remember it without looking at the parts is Yamaha engineered those connections very well... 

Battery + has a female that protects it from a short to ground

Harness wire that goes to battery has the male...  if it was disconnected from battery and shorted with engine running the power from stator to battery is protected by fuse... 

Same with all the other connections...  either protected from short to ground by being a female connector or protected by fuse if not. 

Thanks to all of you, and in my defense, i did search for this, (i'm sure they're there) but i did not find what i was looking for.

Search is hit and miss, if you don't use the right wording you can get threads that have little to do with what you're looking to find...

"Search is hit and miss, if you don't use the right wording you can get threads that have little to do with what you're looking to find..."

If I remember correctly (not guaranteed!  ), the "Search Forum" button on the lower toolbar is more effective that the "Search" button on the top toolbar.

Hi Alan, I never paid any attention to the search at the bottom.  I'll have to give that a try next time I do a search.

Yes, DEFINITELY make sure you select search forum!  Not just search.